scverse/genomic-features issues and pull requests

#77 - Breaking changes to ibis

Issue - State: open - Opened by emdann 4 months ago
Labels: bug

#76 - Update template to v0.4.0

Pull Request - State: open - Opened by scverse-bot 4 months ago

#75 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 5 months ago

#74 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#73 - Add codespell pre-commit

Pull Request - State: closed - Opened by ivirshup 6 months ago

#72 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#71 - Example where we directly connect to the ensembl servers

Issue - State: open - Opened by ivirshup 6 months ago - 1 comment
Labels: documentation, enhancement, P2🏝

#70 - No more non-unique column names, or non-queryable columns in list_columns

Pull Request - State: closed - Opened by ivirshup 6 months ago - 1 comment

#69 - add something for pre-commit to fix

Pull Request - State: closed - Opened by ivirshup 6 months ago

#68 - add pre-commit CI

Issue - State: closed - Opened by ivirshup 6 months ago
Labels: enhancement

#67 - Some cleanup on the ensembldb code

Pull Request - State: closed - Opened by gamazeps 6 months ago - 1 comment

#66 - Add UCSC TxDb

Pull Request - State: open - Opened by gamazeps 6 months ago - 3 comments

#65 - Add Chip_seq_genomic_ranges_tutorial

Pull Request - State: closed - Opened by vmuckerson 6 months ago - 7 comments

#64 - Sort output

Pull Request - State: open - Opened by thomas-reimonn 6 months ago - 4 comments

#63 - `return_type`

Issue - State: open - Opened by ivirshup 6 months ago
Labels: enhancement, P1☕️, API

#62 - What order should results be in?

Issue - State: open - Opened by ivirshup 6 months ago - 7 comments
Labels: enhancement, P0‼️, API

#61 - Better downloads

Issue - State: open - Opened by ivirshup 6 months ago - 1 comment
Labels: enhancement, P2🏝, performance 🐌

#60 - Fix import

Pull Request - State: closed - Opened by ivirshup 6 months ago - 1 comment

#59 - Feat: Use duckdb as backend instead of sqlite

Pull Request - State: closed - Opened by thomas-reimonn 6 months ago - 3 comments
Labels: performance 🐌

#58 - Test against duckdb

Issue - State: closed - Opened by ivirshup 6 months ago - 8 comments
Labels: enhancement, P2🏝, performance 🐌

#57 - Fix: Add tqdm dependency and remove prettier from pre-commit

Pull Request - State: closed - Opened by thomas-reimonn 6 months ago - 2 comments

#56 - Update template to v0.3.1

Pull Request - State: closed - Opened by scverse-bot 7 months ago - 2 comments

#55 - Update template to v0.3.0

Pull Request - State: closed - Opened by scverse-bot 10 months ago

#54 - Renaming

Pull Request - State: open - Opened by ivirshup about 1 year ago - 1 comment

#53 - Update template to v0.2.22

Pull Request - State: closed - Opened by scverse-bot about 1 year ago

#52 - Update template to v0.2.21

Pull Request - State: closed - Opened by scverse-bot about 1 year ago

#51 - Fix rendering of method parameters

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: bug, documentation

#50 - Remove Filter.required_tables method

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#49 - Reduce EnsemblDB public interface

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#48 - Make internal EnsemblDB methods private

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement

#47 - Finalizing names

Issue - State: open - Opened by ivirshup over 1 year ago
Labels: enhancement, P0‼️, API

#46 - Return better dtypes

Issue - State: open - Opened by ivirshup over 1 year ago
Labels: enhancement, P0‼️, performance 🐌

#45 - Transcription Factor column

Issue - State: open - Opened by james-cranley over 1 year ago - 1 comment
Labels: enhancement

#44 - `transcripts`, `exons` functions + some filters

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 3 comments
Labels: enhancement

#43 - Providing access to protein annotations and general note

Issue - State: open - Opened by jorainer over 1 year ago - 2 comments
Labels: enhancement

#42 - `list_columns` includes columns from `"metadata"` and `"chromosome"` table

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: bug

#41 - codecov badge

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation, CI

#40 - Use more features in basic tutorial

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 2 comments
Labels: documentation

#39 - Add opengraph support to docs

Pull Request - State: closed - Opened by ivirshup over 1 year ago
Labels: documentation

#38 - Add simple repr for EnsemblDB

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#37 - Add pypi badge

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation

#36 - Update authors

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 2 comments

#35 - Add functionality to join three tables that are partially related

Issue - State: closed - Opened by lauradmartens over 1 year ago - 1 comment
Labels: enhancement

#34 - Get table of promoter region

Pull Request - State: open - Opened by emdann over 1 year ago - 1 comment

#33 - Defining the main genomic coordinates for each table

Issue - State: open - Opened by emdann over 1 year ago - 2 comments
Labels: enhancement, P1☕️

#32 - Filter by genomic range

Pull Request - State: closed - Opened by emdann over 1 year ago - 5 comments

#31 - Add more filters

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 2 comments

#30 - User guide section: filters

Issue - State: open - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation, enhancement

#29 - Filter negation

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#28 - Pandas intersphinx fix

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation

#27 - More filters

Issue - State: open - Opened by ivirshup over 1 year ago
Labels: enhancement

#26 - API doc headings

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 2 comments

#25 - Doc filters + fix docs

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation

#24 - Add filter examples to basic usage notebook

Issue - State: closed - Opened by emdann over 1 year ago - 2 comments
Labels: enhancement

#23 - Add gene annotations to anndata vars

Pull Request - State: open - Opened by emdann over 1 year ago - 5 comments

#22 - Initial columns functions

Pull Request - State: closed - Opened by lauradmartens over 1 year ago - 4 comments

#21 - Utility function to list available Ensembl versions for species

Pull Request - State: closed - Opened by emdann over 1 year ago - 2 comments

#20 - Change repo name

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#19 - Rename to genomic-features

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#18 - Initial filters

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 2 comments

#17 - List available dbs

Issue - State: closed - Opened by ivirshup over 1 year ago
Labels: enhancement, P0‼️

#16 - Missing ensembl versions

Issue - State: open - Opened by emdann over 1 year ago - 4 comments
Labels: bug, P1☕️

#15 - How tos

Issue - State: open - Opened by ivirshup over 1 year ago
Labels: documentation, enhancement, P1☕️

#14 - annotate_anndata/ annotate_table

Issue - State: open - Opened by ivirshup over 1 year ago
Labels: enhancement, P1☕️

#13 - Get sequences

Issue - State: open - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement, P2🏝

#12 - `genes`, `transcripts`, `exons` functions

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement, P0‼️

#11 - UCSC databases (TxDB)

Issue - State: open - Opened by ivirshup over 1 year ago - 2 comments
Labels: enhancement, P2🏝

#10 - filter argument

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement, P0‼️

#9 - columns argument (plus joins)

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement, P0‼️

#8 - Lift-over between genome versions

Issue - State: closed - Opened by emdann over 1 year ago - 1 comment
Labels: enhancement, P2🏝

#7 - Conversion of seqlevel styles

Issue - State: open - Opened by lauradmartens over 1 year ago - 2 comments
Labels: enhancement, P2🏝

#6 - Discoverability of features

Issue - State: closed - Opened by ivirshup over 1 year ago - 2 comments
Labels: enhancement, meta

#5 - Add link to design doc

Pull Request - State: closed - Opened by ivirshup over 1 year ago

#4 - TSS/ promoter regions

Issue - State: open - Opened by ivirshup over 1 year ago - 2 comments
Labels: enhancement, P1☕️

#3 - Public doc builds

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: documentation, enhancement, P0‼️

#2 - Package name

Issue - State: closed - Opened by ivirshup over 1 year ago - 1 comment
Labels: enhancement, P0‼️

#1 - First features

Pull Request - State: closed - Opened by ivirshup over 1 year ago - 1 comment

GitHub / scverse/genomic-features issues and pull requests